Starting phenix.real_space_refine on Fri Sep 11 22:39:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.cif Found real_map, /net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.map" model { file = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7elc_31180/09_2026/7elc_31180.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 4 6.06 5 P 7 5.49 5 S 83 5.16 5 C 7458 2.51 5 N 2002 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11754 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11193 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 39, 'TRANS': 1369} Chain breaks: 15 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 5, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2014 SG CYS A 284 50.115 66.499 25.945 1.00 39.04 S ATOM 2038 SG CYS A 287 53.363 66.957 23.538 1.00 38.92 S ATOM 3378 SG CYS A 470 49.797 68.522 22.607 1.00 67.43 S ATOM 9952 SG CYS A1650 39.911 15.154 42.832 1.00 76.77 S ATOM 9965 SG CYS A1652 36.471 15.298 43.227 1.00 78.38 S ATOM 9984 SG CYS A1655 39.918 18.510 43.735 1.00 66.72 S ATOM 10056 SG CYS A1664 38.079 16.333 45.513 1.00 59.44 S ATOM 11254 SG CYS B 39 23.348 77.702 52.665 1.00 45.38 S ATOM 11275 SG CYS B 42 25.973 79.094 51.654 1.00 44.44 S ATOM 11409 SG CYS B 58 21.496 79.659 50.588 1.00 59.01 S ATOM 11434 SG CYS B 61 23.404 77.092 49.258 1.00 58.68 S ATOM 11357 SG CYS B 52 16.244 70.508 55.345 1.00 68.57 S ATOM 11524 SG CYS B 72 18.943 69.558 53.533 1.00 53.78 S ATOM 11548 SG CYS B 75 18.152 67.872 56.362 1.00 52.91 S Time building chain proxies: 2.19, per 1000 atoms: 0.19 Number of scatterers: 11754 At special positions: 0 Unit cell: (119, 110, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Mn 1 24.99 S 83 16.00 P 7 15.00 O 2199 8.00 N 2002 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 545.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " Number of angles added : 18 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 52.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 4.014A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.751A pdb=" N ALA A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.763A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.930A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.860A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.536A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.750A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.688A pdb=" N ASP A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.550A pdb=" N LYS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.872A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 501 removed outlier: 3.525A pdb=" N GLN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 579 through 583 removed outlier: 4.392A pdb=" N PHE A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.777A pdb=" N LEU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.519A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.722A pdb=" N VAL A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.894A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 4.227A pdb=" N MET A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1248 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 4.381A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.522A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.580A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1514 through 1520 Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 4.247A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.522A pdb=" N LEU A1668 " --> pdb=" O ASN A1665 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1665 through 1669' Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.575A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1698 Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1774 through 1783 removed outlier: 3.549A pdb=" N ALA A1778 " --> pdb=" O ASP A1774 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1780 " --> pdb=" O CYS A1776 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A1783 " --> pdb=" O LEU A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'B' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.011A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.290A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.633A pdb=" N CYS A 528 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 553 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 572 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 555 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 570 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 557 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 735 through 736 removed outlier: 6.941A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 553 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3765 1.34 - 1.46: 2121 1.46 - 1.58: 5955 1.58 - 1.70: 13 1.70 - 1.82: 116 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP A1470 " pdb=" CB ASP A1470 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.09e-01 bond pdb=" CB ASP A1470 " pdb=" CG ASP A1470 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.68e-01 bond pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 1.550 1.542 0.009 1.03e-02 9.43e+03 7.20e-01 bond pdb=" C ARG A 691 " pdb=" O ARG A 691 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 7.18e-01 bond pdb=" CB VAL A 358 " pdb=" CG1 VAL A 358 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.23e-01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 15922 1.89 - 3.77: 209 3.77 - 5.66: 29 5.66 - 7.54: 5 7.54 - 9.43: 1 Bond angle restraints: 16166 Sorted by residual: angle pdb=" N GLU A 427 " pdb=" CA GLU A 427 " pdb=" C GLU A 427 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.90e+01 angle pdb=" C CYS B 42 " pdb=" N TRP B 43 " pdb=" CA TRP B 43 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.73e+00 angle pdb=" CA TRP B 43 " pdb=" CB TRP B 43 " pdb=" CG TRP B 43 " ideal model delta sigma weight residual 113.60 118.98 -5.38 1.90e+00 2.77e-01 8.02e+00 angle pdb=" CA GLU A 427 " pdb=" C GLU A 427 " pdb=" N ILE A 428 " ideal model delta sigma weight residual 119.26 116.16 3.10 1.14e+00 7.69e-01 7.40e+00 angle pdb=" CA LEU A 435 " pdb=" CB LEU A 435 " pdb=" CG LEU A 435 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.26e+00 ... (remaining 16161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6510 17.97 - 35.94: 560 35.94 - 53.91: 138 53.91 - 71.87: 33 71.87 - 89.84: 9 Dihedral angle restraints: 7250 sinusoidal: 2998 harmonic: 4252 Sorted by residual: dihedral pdb=" C4' C C 18 " pdb=" C3' C C 18 " pdb=" C2' C C 18 " pdb=" C1' C C 18 " ideal model delta sinusoidal sigma weight residual 36.34 -34.78 71.12 1 3.10e+00 1.04e-01 6.76e+02 dihedral pdb=" C4' U C 16 " pdb=" C3' U C 16 " pdb=" C2' U C 16 " pdb=" C1' U C 16 " ideal model delta sinusoidal sigma weight residual 36.34 -34.28 70.63 1 3.10e+00 1.04e-01 6.68e+02 dihedral pdb=" O4' C C 18 " pdb=" C4' C C 18 " pdb=" C3' C C 18 " pdb=" C2' C C 18 " ideal model delta sinusoidal sigma weight residual -35.15 24.45 -59.59 1 4.00e+00 6.25e-02 2.96e+02 ... (remaining 7247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1586 0.055 - 0.111: 240 0.111 - 0.166: 21 0.166 - 0.222: 1 0.222 - 0.277: 10 Chirality restraints: 1858 Sorted by residual: chirality pdb=" C2' C C 18 " pdb=" C3' C C 18 " pdb=" O2' C C 18 " pdb=" C1' C C 18 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' U C 16 " pdb=" C3' U C 16 " pdb=" O2' U C 16 " pdb=" C1' U C 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" P G C 15 " pdb=" OP1 G C 15 " pdb=" OP2 G C 15 " pdb=" O5' G C 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1855 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1280 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A1281 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A1281 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1281 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1753 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A1754 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1754 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1754 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 710 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 711 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 711 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 711 " 0.017 5.00e-02 4.00e+02 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 969 2.74 - 3.28: 12104 3.28 - 3.82: 19734 3.82 - 4.36: 24062 4.36 - 4.90: 40471 Nonbonded interactions: 97340 Sorted by model distance: nonbonded pdb=" OD1 ASP A 769 " pdb=" OG1 THR A 772 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 538 " pdb=" OD1 ASN A 562 " model vdw 2.235 3.040 nonbonded pdb=" O ASP A 370 " pdb=" OG SER A 374 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A1420 " pdb=" NH1 ARG A1476 " model vdw 2.237 3.120 nonbonded pdb=" O LYS A1191 " pdb=" OG1 THR A1195 " model vdw 2.250 3.040 ... (remaining 97335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 11988 Z= 0.154 Angle : 0.974 55.476 16188 Z= 0.345 Chirality : 0.044 0.277 1858 Planarity : 0.003 0.035 2014 Dihedral : 14.860 89.844 4472 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 2.73 % Allowed : 9.64 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.20), residues: 1424 helix: -0.84 (0.17), residues: 733 sheet: -2.89 (0.39), residues: 104 loop : -3.40 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 36 TYR 0.009 0.001 TYR A 534 PHE 0.018 0.001 PHE A 533 TRP 0.008 0.001 TRP A1680 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11970) covalent geometry : angle 0.56197 / 0.31 (16166) SS BOND : bond 0.00153 / 0.08 ( 2) SS BOND : angle 3.02124 / 1.63 ( 4) hydrogen bonds : bond 0.12713 / 8.46 ( 553) hydrogen bonds : angle 5.74536 / 3.97 ( 1593) metal coordination : bond 0.06536 / 3.68 ( 16) metal coordination : angle 23.82586 / 12.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 357 MET cc_start: 0.8158 (tpp) cc_final: 0.7516 (mmt) REVERT: A 766 ASP cc_start: 0.7883 (p0) cc_final: 0.7635 (p0) REVERT: A 1143 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6681 (tpp80) REVERT: A 1272 GLN cc_start: 0.7779 (mt0) cc_final: 0.7479 (mt0) REVERT: A 1391 GLU cc_start: 0.7493 (pt0) cc_final: 0.7148 (pm20) REVERT: A 1414 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 1527 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 1625 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7546 (mmp) REVERT: B 65 MET cc_start: 0.8039 (mtm) cc_final: 0.7761 (mtm) REVERT: B 68 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6129 (p0) outliers start: 36 outliers final: 23 residues processed: 250 average time/residue: 0.1284 time to fit residues: 44.3621 Evaluate side-chains 199 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 125 ASN A 148 ASN A 185 GLN A 189 HIS A 359 ASN A 442 ASN A 522 ASN A 546 GLN A 628 ASN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN A 788 ASN A1128 ASN A1206 GLN A1231 HIS A1275 GLN A1283 HIS A1296 HIS A1463 GLN A1496 ASN A1551 ASN A1712 ASN A1726 GLN A1743 ASN A1783 ASN A1791 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140699 restraints weight = 13331.467| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.99 r_work: 0.3352 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11988 Z= 0.165 Angle : 0.733 28.840 16188 Z= 0.317 Chirality : 0.045 0.481 1858 Planarity : 0.004 0.041 2014 Dihedral : 8.913 131.122 1686 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.11 % Favored : 89.82 % Rotamer: Outliers : 3.57 % Allowed : 12.97 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.22), residues: 1424 helix: 0.07 (0.18), residues: 750 sheet: -2.63 (0.43), residues: 101 loop : -3.04 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 551 TYR 0.012 0.001 TYR A 572 PHE 0.023 0.002 PHE A1511 TRP 0.010 0.001 TRP A1549 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (11970) covalent geometry : angle 0.63371 / 0.31 (16166) SS BOND : bond 0.00635 / 0.30 ( 2) SS BOND : angle 2.89048 / 1.52 ( 4) hydrogen bonds : bond 0.03539 / 2.43 ( 553) hydrogen bonds : angle 4.67988 / 3.23 ( 1593) metal coordination : bond 0.02177 / 1.51 ( 16) metal coordination : angle 10.98010 / 6.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.469 Fit side-chains REVERT: A 120 MET cc_start: 0.6592 (tpp) cc_final: 0.6321 (tpt) REVERT: A 357 MET cc_start: 0.8378 (tpp) cc_final: 0.7787 (mmt) REVERT: A 381 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6627 (tt) REVERT: A 384 GLN cc_start: 0.6499 (mm-40) cc_final: 0.6296 (mm-40) REVERT: A 1143 ARG cc_start: 0.7504 (tmm-80) cc_final: 0.6530 (tpp80) REVERT: A 1272 GLN cc_start: 0.7733 (mt0) cc_final: 0.6931 (mm-40) REVERT: A 1307 GLU cc_start: 0.8072 (tp30) cc_final: 0.7653 (tp30) REVERT: A 1391 GLU cc_start: 0.7803 (pt0) cc_final: 0.6940 (pm20) REVERT: A 1462 ASP cc_start: 0.7250 (t0) cc_final: 0.6918 (t0) REVERT: A 1488 ASP cc_start: 0.7846 (p0) cc_final: 0.7618 (p0) REVERT: A 1527 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 36 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7129 (ptt-90) REVERT: B 65 MET cc_start: 0.8009 (mtm) cc_final: 0.7727 (mtm) REVERT: B 68 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6135 (p0) REVERT: B 70 GLU cc_start: 0.7762 (tp30) cc_final: 0.7046 (tp30) outliers start: 47 outliers final: 34 residues processed: 227 average time/residue: 0.1135 time to fit residues: 37.3713 Evaluate side-chains 203 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 189 HIS A 335 ASN A 359 ASN A 438 GLN A 476 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1331 GLN A1726 GLN A1734 ASN A1812 HIS ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.171706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133485 restraints weight = 13649.125| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.99 r_work: 0.3289 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11988 Z= 0.228 Angle : 0.750 24.428 16188 Z= 0.332 Chirality : 0.047 0.433 1858 Planarity : 0.004 0.046 2014 Dihedral : 9.022 139.245 1682 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.53 % Favored : 89.40 % Rotamer: Outliers : 4.40 % Allowed : 16.08 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.22), residues: 1424 helix: 0.24 (0.18), residues: 752 sheet: -2.44 (0.45), residues: 100 loop : -2.93 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 551 TYR 0.011 0.002 TYR A 695 PHE 0.022 0.002 PHE A 533 TRP 0.012 0.002 TRP B 43 HIS 0.006 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (11970) covalent geometry : angle 0.66238 / 0.32 (16166) SS BOND : bond 0.00414 / 0.20 ( 2) SS BOND : angle 2.07803 / 1.43 ( 4) hydrogen bonds : bond 0.03784 / 2.58 ( 553) hydrogen bonds : angle 4.65733 / 3.20 ( 1593) metal coordination : bond 0.01882 / 1.28 ( 16) metal coordination : angle 10.51698 / 5.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.538 Fit side-chains REVERT: A 166 GLU cc_start: 0.4284 (OUTLIER) cc_final: 0.3993 (mp0) REVERT: A 381 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6790 (tt) REVERT: A 775 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9044 (p) REVERT: A 1143 ARG cc_start: 0.7480 (tmm-80) cc_final: 0.6484 (tpp80) REVERT: A 1268 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5944 (tp30) REVERT: A 1272 GLN cc_start: 0.7874 (mt0) cc_final: 0.7536 (mt0) REVERT: A 1307 GLU cc_start: 0.8202 (tp30) cc_final: 0.7634 (tp30) REVERT: A 1391 GLU cc_start: 0.7849 (pt0) cc_final: 0.6943 (pm20) REVERT: A 1462 ASP cc_start: 0.7293 (t0) cc_final: 0.6981 (t0) REVERT: A 1488 ASP cc_start: 0.8102 (p0) cc_final: 0.7878 (p0) REVERT: A 1527 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 36 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7339 (ptt-90) REVERT: B 65 MET cc_start: 0.7901 (mtm) cc_final: 0.7646 (mtm) REVERT: B 68 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.6284 (p0) outliers start: 58 outliers final: 44 residues processed: 229 average time/residue: 0.1058 time to fit residues: 35.4807 Evaluate side-chains 221 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 87 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 149 ASN A 476 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN A1111 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140037 restraints weight = 13567.885| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.97 r_work: 0.3326 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11988 Z= 0.139 Angle : 0.677 18.506 16188 Z= 0.302 Chirality : 0.044 0.293 1858 Planarity : 0.004 0.046 2014 Dihedral : 8.739 136.994 1682 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.55 % Favored : 90.38 % Rotamer: Outliers : 4.63 % Allowed : 17.75 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.22), residues: 1424 helix: 0.56 (0.19), residues: 750 sheet: -2.18 (0.49), residues: 94 loop : -2.77 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.012 0.001 TYR A 534 PHE 0.025 0.001 PHE A1105 TRP 0.009 0.001 TRP A1549 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (11970) covalent geometry : angle 0.61127 / 0.30 (16166) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 1.81144 / 1.30 ( 4) hydrogen bonds : bond 0.03328 / 2.26 ( 553) hydrogen bonds : angle 4.43837 / 3.05 ( 1593) metal coordination : bond 0.01595 / 1.15 ( 16) metal coordination : angle 8.70299 / 4.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 0.458 Fit side-chains REVERT: A 166 GLU cc_start: 0.4194 (OUTLIER) cc_final: 0.3916 (mp0) REVERT: A 381 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6668 (tt) REVERT: A 1143 ARG cc_start: 0.7447 (tmm-80) cc_final: 0.6450 (tpp80) REVERT: A 1268 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: A 1272 GLN cc_start: 0.7902 (mt0) cc_final: 0.7702 (mt0) REVERT: A 1307 GLU cc_start: 0.7890 (tp30) cc_final: 0.7432 (tp30) REVERT: A 1391 GLU cc_start: 0.7813 (pt0) cc_final: 0.6928 (pm20) REVERT: A 1462 ASP cc_start: 0.7478 (t0) cc_final: 0.7116 (t0) REVERT: A 1527 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7784 (tp) REVERT: A 1543 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7482 (ttt180) REVERT: A 1657 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8207 (pt) REVERT: B 36 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7383 (ptt-90) REVERT: B 68 ASN cc_start: 0.6832 (OUTLIER) cc_final: 0.6215 (p0) REVERT: B 70 GLU cc_start: 0.7791 (tp30) cc_final: 0.7052 (tp30) outliers start: 61 outliers final: 42 residues processed: 230 average time/residue: 0.1080 time to fit residues: 36.5206 Evaluate side-chains 219 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 189 HIS A 359 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1666 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142015 restraints weight = 13488.015| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.07 r_work: 0.3379 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11988 Z= 0.111 Angle : 0.635 14.765 16188 Z= 0.293 Chirality : 0.042 0.200 1858 Planarity : 0.003 0.045 2014 Dihedral : 8.474 136.460 1682 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.64 % Favored : 91.29 % Rotamer: Outliers : 4.55 % Allowed : 18.21 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1424 helix: 0.86 (0.19), residues: 762 sheet: -2.04 (0.50), residues: 92 loop : -2.72 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.007 0.001 TYR A 695 PHE 0.026 0.001 PHE A1105 TRP 0.008 0.001 TRP A1680 HIS 0.003 0.000 HIS A1405 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11970) covalent geometry : angle 0.58904 / 0.29 (16166) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 4.28370 / 2.50 ( 4) hydrogen bonds : bond 0.03038 / 2.05 ( 553) hydrogen bonds : angle 4.25585 / 2.93 ( 1593) metal coordination : bond 0.01083 / 0.78 ( 16) metal coordination : angle 6.83546 / 3.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.4086 (OUTLIER) cc_final: 0.3829 (mp0) REVERT: A 264 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7774 (mtt-85) REVERT: A 381 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6495 (tt) REVERT: A 484 MET cc_start: 0.7884 (mmm) cc_final: 0.7439 (mmt) REVERT: A 713 ARG cc_start: 0.7465 (ttt90) cc_final: 0.7102 (tpt90) REVERT: A 736 VAL cc_start: 0.8239 (t) cc_final: 0.7974 (t) REVERT: A 1138 THR cc_start: 0.8823 (t) cc_final: 0.8609 (t) REVERT: A 1143 ARG cc_start: 0.7327 (tmm-80) cc_final: 0.6296 (tpp80) REVERT: A 1179 ASN cc_start: 0.8481 (m-40) cc_final: 0.8237 (m110) REVERT: A 1268 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6038 (mm-30) REVERT: A 1307 GLU cc_start: 0.7759 (tp30) cc_final: 0.7300 (tp30) REVERT: A 1391 GLU cc_start: 0.7487 (pt0) cc_final: 0.6665 (pm20) REVERT: A 1657 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 36 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7357 (ptt-90) REVERT: B 68 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6268 (p0) REVERT: B 70 GLU cc_start: 0.7789 (tp30) cc_final: 0.7038 (tp30) outliers start: 60 outliers final: 38 residues processed: 232 average time/residue: 0.1070 time to fit residues: 36.5586 Evaluate side-chains 213 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 138 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 189 HIS A 425 HIS A 546 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.178206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.140965 restraints weight = 13458.899| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.98 r_work: 0.3372 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11988 Z= 0.137 Angle : 0.660 16.550 16188 Z= 0.304 Chirality : 0.044 0.212 1858 Planarity : 0.004 0.045 2014 Dihedral : 8.261 136.050 1675 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 4.40 % Allowed : 19.04 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1424 helix: 0.93 (0.19), residues: 762 sheet: -1.90 (0.50), residues: 92 loop : -2.64 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 404 TYR 0.011 0.001 TYR A1312 PHE 0.029 0.001 PHE A1105 TRP 0.009 0.001 TRP B 43 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (11970) covalent geometry : angle 0.60504 / 0.30 (16166) SS BOND : bond 0.00335 / 0.17 ( 2) SS BOND : angle 5.90810 / 3.31 ( 4) hydrogen bonds : bond 0.03137 / 2.12 ( 553) hydrogen bonds : angle 4.25897 / 2.93 ( 1593) metal coordination : bond 0.01328 / 0.93 ( 16) metal coordination : angle 7.41844 / 4.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.4187 (OUTLIER) cc_final: 0.3886 (mp0) REVERT: A 264 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7839 (mtt-85) REVERT: A 381 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6675 (tt) REVERT: A 484 MET cc_start: 0.7936 (mmm) cc_final: 0.7483 (mmt) REVERT: A 713 ARG cc_start: 0.7535 (ttt90) cc_final: 0.7181 (tpt90) REVERT: A 743 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7645 (mtmm) REVERT: A 1143 ARG cc_start: 0.7410 (tmm-80) cc_final: 0.6425 (tpp80) REVERT: A 1179 ASN cc_start: 0.8495 (m-40) cc_final: 0.8238 (m110) REVERT: A 1268 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6017 (mm-30) REVERT: A 1272 GLN cc_start: 0.7611 (mt0) cc_final: 0.6853 (mm-40) REVERT: A 1307 GLU cc_start: 0.7795 (tp30) cc_final: 0.7344 (tp30) REVERT: A 1391 GLU cc_start: 0.7502 (pt0) cc_final: 0.6729 (pm20) REVERT: A 1462 ASP cc_start: 0.7468 (t0) cc_final: 0.7092 (t0) REVERT: A 1657 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8194 (pt) REVERT: B 68 ASN cc_start: 0.6946 (OUTLIER) cc_final: 0.6393 (p0) REVERT: B 70 GLU cc_start: 0.7791 (tp30) cc_final: 0.7031 (tp30) outliers start: 58 outliers final: 46 residues processed: 218 average time/residue: 0.1094 time to fit residues: 35.1353 Evaluate side-chains 221 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140733 restraints weight = 13381.014| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.05 r_work: 0.3357 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11988 Z= 0.150 Angle : 0.662 15.563 16188 Z= 0.306 Chirality : 0.044 0.228 1858 Planarity : 0.004 0.046 2014 Dihedral : 8.175 135.954 1671 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 4.25 % Allowed : 19.65 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1424 helix: 0.95 (0.19), residues: 762 sheet: -1.82 (0.50), residues: 92 loop : -2.58 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.014 0.001 TYR A 534 PHE 0.033 0.002 PHE A1105 TRP 0.011 0.001 TRP B 43 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11970) covalent geometry : angle 0.61358 / 0.30 (16166) SS BOND : bond 0.01035 / 0.54 ( 2) SS BOND : angle 3.58670 / 2.20 ( 4) hydrogen bonds : bond 0.03174 / 2.15 ( 553) hydrogen bonds : angle 4.26931 / 2.94 ( 1593) metal coordination : bond 0.01311 / 0.93 ( 16) metal coordination : angle 7.32339 / 3.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.459 Fit side-chains REVERT: A 166 GLU cc_start: 0.4293 (OUTLIER) cc_final: 0.3984 (mp0) REVERT: A 264 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7858 (mtt-85) REVERT: A 381 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6682 (tt) REVERT: A 713 ARG cc_start: 0.7586 (ttt90) cc_final: 0.7227 (tpt90) REVERT: A 743 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7623 (mtmm) REVERT: A 1143 ARG cc_start: 0.7391 (tmm-80) cc_final: 0.6373 (tpp80) REVERT: A 1179 ASN cc_start: 0.8527 (m-40) cc_final: 0.8282 (m110) REVERT: A 1268 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6050 (mm-30) REVERT: A 1272 GLN cc_start: 0.7583 (mt0) cc_final: 0.6843 (mm-40) REVERT: A 1307 GLU cc_start: 0.7888 (tp30) cc_final: 0.7405 (tp30) REVERT: A 1462 ASP cc_start: 0.7531 (t0) cc_final: 0.7147 (t0) REVERT: A 1657 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8161 (pt) REVERT: B 68 ASN cc_start: 0.6934 (OUTLIER) cc_final: 0.6406 (p0) REVERT: B 70 GLU cc_start: 0.7811 (tp30) cc_final: 0.7070 (tp30) outliers start: 56 outliers final: 46 residues processed: 213 average time/residue: 0.1090 time to fit residues: 34.2525 Evaluate side-chains 226 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 141 optimal weight: 0.0070 chunk 103 optimal weight: 0.4980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 737 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142124 restraints weight = 13366.549| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.04 r_work: 0.3472 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11988 Z= 0.122 Angle : 0.642 14.236 16188 Z= 0.297 Chirality : 0.043 0.198 1858 Planarity : 0.004 0.045 2014 Dihedral : 8.101 135.939 1670 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.17 % Allowed : 20.18 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1424 helix: 1.04 (0.19), residues: 762 sheet: -1.90 (0.51), residues: 90 loop : -2.54 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.008 0.001 TYR A 695 PHE 0.034 0.001 PHE A1105 TRP 0.008 0.001 TRP A1680 HIS 0.004 0.000 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (11970) covalent geometry : angle 0.59790 / 0.29 (16166) SS BOND : bond 0.00720 / 0.38 ( 2) SS BOND : angle 2.75742 / 1.79 ( 4) hydrogen bonds : bond 0.03024 / 2.04 ( 553) hydrogen bonds : angle 4.20990 / 2.90 ( 1593) metal coordination : bond 0.01259 / 0.91 ( 16) metal coordination : angle 6.92989 / 3.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.504 Fit side-chains REVERT: A 166 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.4022 (mp0) REVERT: A 264 ARG cc_start: 0.8305 (mtp180) cc_final: 0.8091 (mtt-85) REVERT: A 357 MET cc_start: 0.8413 (mmm) cc_final: 0.7934 (mmt) REVERT: A 381 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6851 (tt) REVERT: A 422 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 484 MET cc_start: 0.7850 (mmm) cc_final: 0.7568 (mmt) REVERT: A 595 MET cc_start: 0.8880 (mmm) cc_final: 0.8312 (mtt) REVERT: A 713 ARG cc_start: 0.7763 (ttt90) cc_final: 0.7448 (tpt90) REVERT: A 743 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7636 (mtmm) REVERT: A 1143 ARG cc_start: 0.7646 (tmm-80) cc_final: 0.6711 (tpp80) REVERT: A 1179 ASN cc_start: 0.8510 (m-40) cc_final: 0.8290 (m110) REVERT: A 1268 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6125 (mm-30) REVERT: A 1272 GLN cc_start: 0.7853 (mt0) cc_final: 0.7106 (mm-40) REVERT: A 1307 GLU cc_start: 0.7815 (tp30) cc_final: 0.7542 (tp30) REVERT: A 1657 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8122 (pt) REVERT: B 68 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.6503 (p0) REVERT: B 70 GLU cc_start: 0.7832 (tp30) cc_final: 0.7042 (tp30) outliers start: 55 outliers final: 46 residues processed: 218 average time/residue: 0.1106 time to fit residues: 35.3397 Evaluate side-chains 223 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1411 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 141 optimal weight: 0.0570 chunk 40 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN A 189 HIS A 546 GLN A 737 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143893 restraints weight = 13417.387| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.97 r_work: 0.3390 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11988 Z= 0.121 Angle : 0.650 13.349 16188 Z= 0.300 Chirality : 0.043 0.196 1858 Planarity : 0.004 0.046 2014 Dihedral : 8.065 135.610 1670 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.17 % Allowed : 20.26 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1424 helix: 1.12 (0.19), residues: 760 sheet: -1.86 (0.50), residues: 90 loop : -2.51 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 144 TYR 0.007 0.001 TYR A 695 PHE 0.034 0.001 PHE A1105 TRP 0.007 0.001 TRP A1680 HIS 0.004 0.000 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11970) covalent geometry : angle 0.61040 / 0.30 (16166) SS BOND : bond 0.00677 / 0.35 ( 2) SS BOND : angle 2.66062 / 1.74 ( 4) hydrogen bonds : bond 0.02979 / 2.01 ( 553) hydrogen bonds : angle 4.18241 / 2.88 ( 1593) metal coordination : bond 0.01178 / 0.85 ( 16) metal coordination : angle 6.64020 / 3.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.467 Fit side-chains REVERT: A 144 ARG cc_start: 0.6446 (mtm-85) cc_final: 0.4882 (mmp-170) REVERT: A 166 GLU cc_start: 0.4199 (OUTLIER) cc_final: 0.3890 (mp0) REVERT: A 264 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7890 (mtt-85) REVERT: A 357 MET cc_start: 0.8320 (mmm) cc_final: 0.7852 (mmt) REVERT: A 381 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6681 (tt) REVERT: A 422 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 484 MET cc_start: 0.7924 (mmm) cc_final: 0.7528 (mmt) REVERT: A 595 MET cc_start: 0.8918 (mmm) cc_final: 0.8344 (mtt) REVERT: A 606 MET cc_start: 0.8786 (ptm) cc_final: 0.8523 (ptt) REVERT: A 713 ARG cc_start: 0.7582 (ttt90) cc_final: 0.7300 (tpt90) REVERT: A 743 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7524 (mtmm) REVERT: A 1143 ARG cc_start: 0.7368 (tmm-80) cc_final: 0.6360 (tpp80) REVERT: A 1179 ASN cc_start: 0.8491 (m-40) cc_final: 0.8226 (m110) REVERT: A 1268 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6038 (mm-30) REVERT: A 1272 GLN cc_start: 0.7751 (mt0) cc_final: 0.7012 (mm-40) REVERT: A 1307 GLU cc_start: 0.7816 (tp30) cc_final: 0.7403 (tp30) REVERT: A 1657 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8191 (pt) REVERT: B 68 ASN cc_start: 0.6986 (OUTLIER) cc_final: 0.6453 (p0) REVERT: B 70 GLU cc_start: 0.7814 (tp30) cc_final: 0.7027 (tp30) outliers start: 55 outliers final: 48 residues processed: 213 average time/residue: 0.1054 time to fit residues: 33.0516 Evaluate side-chains 223 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1411 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142203 restraints weight = 13618.053| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.95 r_work: 0.3343 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11988 Z= 0.156 Angle : 0.676 14.402 16188 Z= 0.311 Chirality : 0.044 0.233 1858 Planarity : 0.004 0.046 2014 Dihedral : 8.091 135.192 1669 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.87 % Allowed : 20.33 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1424 helix: 1.07 (0.19), residues: 754 sheet: -1.85 (0.50), residues: 90 loop : -2.47 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.009 0.001 TYR A 545 PHE 0.034 0.002 PHE A1105 TRP 0.010 0.001 TRP B 43 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (11970) covalent geometry : angle 0.63470 / 0.31 (16166) SS BOND : bond 0.00628 / 0.32 ( 2) SS BOND : angle 2.51419 / 1.68 ( 4) hydrogen bonds : bond 0.03145 / 2.12 ( 553) hydrogen bonds : angle 4.22640 / 2.90 ( 1593) metal coordination : bond 0.01314 / 0.93 ( 16) metal coordination : angle 6.87781 / 3.69 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.492 Fit side-chains REVERT: A 144 ARG cc_start: 0.6324 (mtm-85) cc_final: 0.4788 (mmp-170) REVERT: A 166 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3859 (mp0) REVERT: A 264 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7814 (mtt-85) REVERT: A 357 MET cc_start: 0.8246 (mmm) cc_final: 0.7822 (mmt) REVERT: A 381 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 595 MET cc_start: 0.8931 (mmm) cc_final: 0.8367 (mtt) REVERT: A 606 MET cc_start: 0.8748 (ptm) cc_final: 0.8459 (ptt) REVERT: A 713 ARG cc_start: 0.7543 (ttt90) cc_final: 0.7201 (tpt90) REVERT: A 1143 ARG cc_start: 0.7340 (tmm-80) cc_final: 0.6267 (tpp80) REVERT: A 1169 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7865 (ttp80) REVERT: A 1179 ASN cc_start: 0.8508 (m-40) cc_final: 0.8232 (m110) REVERT: A 1268 GLU cc_start: 0.6872 (mp0) cc_final: 0.6029 (mm-30) REVERT: A 1272 GLN cc_start: 0.7707 (mt0) cc_final: 0.6970 (mm-40) REVERT: A 1307 GLU cc_start: 0.7881 (tp30) cc_final: 0.7383 (tp30) REVERT: A 1462 ASP cc_start: 0.7528 (t0) cc_final: 0.7195 (t0) REVERT: A 1657 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8156 (pt) REVERT: B 68 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.6433 (p0) REVERT: B 70 GLU cc_start: 0.7775 (tp30) cc_final: 0.6986 (tp30) outliers start: 51 outliers final: 47 residues processed: 208 average time/residue: 0.1104 time to fit residues: 33.7369 Evaluate side-chains 219 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1411 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140526 restraints weight = 13548.922| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.01 r_work: 0.3370 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11988 Z= 0.160 Angle : 0.685 15.122 16188 Z= 0.315 Chirality : 0.044 0.249 1858 Planarity : 0.004 0.046 2014 Dihedral : 8.125 135.167 1669 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 4.10 % Allowed : 20.49 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1424 helix: 0.99 (0.19), residues: 762 sheet: -1.87 (0.50), residues: 90 loop : -2.53 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 551 TYR 0.008 0.001 TYR A 214 PHE 0.034 0.002 PHE A1105 TRP 0.011 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (11970) covalent geometry : angle 0.64321 / 0.31 (16166) SS BOND : bond 0.00558 / 0.29 ( 2) SS BOND : angle 2.42461 / 1.65 ( 4) hydrogen bonds : bond 0.03194 / 2.15 ( 553) hydrogen bonds : angle 4.25767 / 2.92 ( 1593) metal coordination : bond 0.01333 / 0.94 ( 16) metal coordination : angle 7.02823 / 3.77 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3655.47 seconds wall clock time: 63 minutes 34.06 seconds (3814.06 seconds total)